This study aimed to analyze the neuronal sources of the visual evoked potentials (VEP) to flash stimuli of the blue- (S-cone) and the red-green (L- and M-cones) color channel of the human visual system. For 11 healthy volunteers a 64 channel electroencephalogram (EEG) was recorded during selective central excitation of S-cones and M- and L-cones. Individual and grand average data were first analyzed topographically. Source localization was then carried out with the help of a realistically shaped three compartment boundary element model and a mirrored moving dipole model restricted to occipital cortex. Two main components, N1 and P1, of blue- and red-green color channel were clearly distinguishable in all subjects. We found a significant latency difference between both stimulation channels for N1 and P1. Results showed no visible differences in the topography and no significant differences in dipole localization between both channels. Talairach coordinates of grand averages indicated activation in area 18. Comparison of results of separately stimulated eyes showed no differences. Our findings revealed that neural processing occurs in the same areas of the visual cortex for stimuli with identical conditions but different spectral properties. The signals of blue- and red-green color channels are transmitted in distinct pathways to the visual cortex, thus the latency differences might be caused by different anatomical and functional properties of these pathways.